Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1043 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0133276668 sf0133275624 1 33276668 1.16E-08 NA
vg0619397284 sf0619396287 6 19397284 1.49E-08 9.02E-06
vg0133316697 sf0133315653 1 33316697 1.97E-08 NA
vg0416033751 sf0415861784 4 16033751 2.80E-08 1.49E-06
vg0102142891 sf0102141891 1 2142891 5.76E-08 NA
vg0619193486 sf0619192489 6 19193486 8.60E-08 3.91E-06
vg0400996445 sf0400991997 4 996445 3.00E-06 NA
vg1105893410 sf1105889162 11 5893410 4.12E-06 NA
vg0133432014 sf0133430970 1 33432014 8.50E-06 NA